Chuck vs The Scrambler
by Kyo Tetsuei
Summary: It seems like every mission that involves Chuck has some kind of inevitable twist. Usually the twists are relatively benign - here's one time it isn't.
1. Teaser

**I don't own Chuck. I'd much rather own NBC, but that's just the psychosis talking.**

* * *

There was only one thing that Sarah Walker and John Casey knew with complete certainty at this very moment, as they sat outside Director Graham's office, waiting to be called in. Muffled arguing could be heard through the door. Whatever Graham and Beckman were yelling about, they were obviously angry enough to bypass the soundproofing of the door, and that led Walker and Casey to the same conclusion:

They were in deep trouble.

* * *

What had started as an almost routine Chuck flash to reveal a Fulcrum development facility merely a few miles away from Langley, Virginia, had turned out to be much more serious than anyone could have ever imagined. As the two agents broke into the abandoned warehouse building, the hairs on the backs of their necks started standing on end – Sarah had never seen anything like it, and Casey let out a growl that tipped Sarah off to something that she knew she wouldn't like. Just as she was about to ask what the issue was, Chuck barreled into the room from behind them, out of breath.

Casey, having seen a similar room before, started to yell at Chuck and moved to push him out of the room. However, Casey was a step too late as all the white walls in the room suddenly exploded into color for less than a second, and then the lighted room went completely dark. Too late, Casey and Sarah watched with horror as Chuck, illuminated only by the light from the doorway, stood ramrod straight for seconds afterward, eyes wide open, face completely blank. Ten seconds after the burst of imagery in the room, Chuck pitched backwards, landing unconscious on the ground.

The subsequent trip to the nearest safe hospital facility was incredibly tense, with Sarah staying by Chuck's side the entire ride, with Casey staying behind to direct the cleanup crews. Soon afterwards, the two had been called to Graham's office, uncertain as to Chuck's situation, and not knowing why they were actually there.

Soon enough, the door opened, and they were admitted into the office, where Sarah's world was turned over again. Chuck had been transferred to the medical center at Bethesda, where the neurology experts there had determined that Chuck had fallen into a coma, with the EEG showing no signs of higher level brain activity.

Chuck had become a vegetable.

* * *

_End Teaser_

8/26/08


	2. Chapter 0 Prologue

**I don't own Chuck, but I really wish I owned NBC.**

* * *

**Chuck vs The Scrambler**

_Chapter 0: Prologue_

_Several months ago, on a nondescript beachside on the East Coast:_

A lone figure stood on a deserted pier, looking out towards the deceptively calm water on a cold post-winter morning. It was maybe half an hour before the sunrise, with the cold March air softly flowing in from off shore. From the sound of it, more than a few birds were already active, ready to herald the coming of the new day. Some were coasting lazily up in the air, and the man wondered if the birds appreciated the salty sea breeze as much as he did. The person on the pier did not need to look at his watch, as right on time, another set of footsteps – sauntering, this time, he observed from the sound of the shoes coming down the pier – came to a halt three steps behind him.

As per established protocol, the man was not allowed to turn around to talk to his contact. He didn't even know the gender of the person, having only heard any words from the veil of a voice synthesizer. A brief moment of humor had the man smirking in the pre-dawn darkness, wondering if his contact looked any bit like Stephen Hawking, but any further speculation had to be abandoned as 'The Voice' started talking.

"As much as I know you enjoy our meetings out here, I know I'd much rather spend this time somewhere not this cold. Have you completed what has been asked of you?"

The man nodded his affirmative reply. A few innocuous lines of code into the single largest electronic undertaking of the US intelligence community since the 'Wolverine' international monitoring algorithm implemented a few years back. Data included into the chatter, to blend in and be processed as just another set of data. Simple, easy, untraceable, and completely harmless. Unless someone specifically activated the trigger, the data would never show up. Simple as pie. Just like the other things he'd added in over the course of a few months.

"Excellent. This will be the last time we meet. You will receive the rest of your payment within 36 hours of verification of successful upload. Should we have need for your services again, we'll be in touch. Have a safe flight home."

With that, the synthesized voice stopped talking, and within seconds, the fading sounds of receding footsteps were masked by the waves crashing against the rocky beach. Turning around, the man finds a leather briefcase on the ground as usual. Picking the briefcase up, he pops it open, and the next thing he feels is a burst of heat as the explosive in the container is triggered, and the man knows no more.

* * *

The line picks up.

"It's done, sir."

A pause.

"Yes, it's ready to be used at any time."

A question from the other end.

"No, he's been taken care of."

Another inquiry.

"No sir, like you mentioned, the program that we've added will lock up any holes that his foreign contacts have asked him to include."

An order.

"Yes sir, I'll be taking care of his other contacts tonight."

Another pause, then three words are spoken.

"Thank you, Director Graham."

* * *

_The scenario was simple. After the events of September 11th, 2001, the CIA and NSA were given an executive order to 'play nice', as the President had put it. The way to do it was through the highly confidential project, a system designed to consolidate the combined resources of two governmental intelligence agencies, with the explicit aim of providing better preparation against potential threats to homeland security. The initial version had gone live less than a year after September 11th, and in addition to regular updates to the information database, there were periodic updates to the system itself, newer and better ways of storing and collating the combined intelligence information contained within what had originally been called the International Terrorism Registry and Support of Counter-Terrorism Project (INTRSCT Project). In recent years, it had just been referred to as the 'Intersect Project', or even just 'the Intersect'._

_The latest revision to the system was using a system hybridized after research from a CIA asset in Stanford University in Palo Alto, California. This research involved taking volumes of raw data and encoding the information into images, which served two functions. First, it provided an extra layer of security for data storage, as instead of schematics, all any potential intrusions would produce were a series of random images. Secondly, a person viewing these images in rapid order would experience a mental overload, disabling anyone without the proper safety precautions from accessing the data._

_To date, no person had been found that could survive the gauntlet of highly encoded graphical data, leading the main researchers to determine that they had found a failsafe method of securing the nation's most important secrets._

_For four years, hostile groups had been unsuccessful in any attempts to retrieve data from the Intersect mainframes for that particular reason. It was not until early in 2007 that an Islamic extremist group was able to make contact with and 'convince' an NSA programmer into adding a few lines of code that would create a backdoor into the secure server housing the information that would decrypt the graphics into base information safe for access._

_Thankfully, an independent CIA audit of the program code had revealed this loophole, and steps had been taken to neutralize this threat with extreme prejudice. The plan had been put in place, and a few months later, the 'situation' had been remedied, with the loophole closed and the source of the problem eliminated. Being that this was the first and only breach of integrity in the Intersect system in over 5 years of activity, the CIA and NSA revised their processes and were back in a good place, as the two agency heads were concerned._

_Little did they know, however, that only a few short months later, they would lose the Intersect altogether through the actions of one rogue agent, and that a new adventure and perilous existence would await a poor Nerd Herd shift supervisor in Southern California…_

* * *

_End Prologue._

* * *

_This update is a bit quick for me, and another chapter that's shorter than what I would have liked, but I wanted to get the teaser and the back story set up before I launched into the actual plot._

8/28/08


	3. Chapter 1: Don't Freak Out

**I don't own Chuck, but I really wish I owned NBC.**

**I own a copy of the Chuck season 1 DVD, but I don't think that counts…**

**

* * *

Chuck vs. the Scrambler**

Chapter 1: Don't Freak Out

* * *

Several months had passed since that fateful day when Chuck had received the Zork-encrypted email from Bryce. In the months since then, Chuck and his two handlers (glorified babysitters, as Casey liked to put it) had been through much together. The trio had thwarted foreign arms dealers, terrorist plots, and turned a foreign agent amongst other achievements. On top of the seemingly 'flavor-of-the-moment' missions, that they had been on, the information stored within Chuck's brain had also proved to be a source of much consternation on top of being beneficial to national security.

More often than not in recent missions, the organization known as Fulcrum seemed to be coming closer and closer to discovering Chuck's true role, something that had both the CIA and NSA increasingly nervous. Bryce's initial successes at uncovering Fulcrum operations and goals seemed to be coming to a standstill. Fulcrum appeared to have gone quiet after their recent failures, and it seemed that Chuck's flash floods of Fulcrum intelligence had turned into a drought. Even the non-Fulcrum information that Chuck was able to supply had slowly started to diminish.

It didn't take too long for the brains in both of the agencies' think tanks to ascertain the reason behind the recent lack of breakthroughs from the 3-person LA juggernaut – the data was old. Before Bryce had destroyed the Intersect computer to prevent Fulcrum access, there was a constant stream of information being supplied to the database from both intelligence agencies, making the Intersect the premier source of information for the US intelligence community. However, after the information had been dumped into Chuck Bartowski's brain, the regular updates had not been maintained. Sure, both agencies were still collecting information, but because they were no longer being stored in a central location, it was effectively hampering the effectiveness of both the CIA and the NSA.

In the modern world where intelligence information frequently had a shelf life of less than three months, this meant that Chuck's information was grossly out of date. This fact had also reared its ugly head in the last two missions where the data in his head had led the three to locations that had been abandoned for some time, leaving them with nothing. Frustrations had started to pile up, and while Chuck knew the real reason, everyone else at home and the Buy More had assumed that Chuck and Sarah were going through a rough patch in their relationship, which to them obviously explained why she wasn't showing up nearly as often as she had in the past.

The Human Intersect wasn't doing too well himself – knowing that his main _raison d'être_ was the rapidly obsolete information in his head, Chuck had fallen into a mini depression of sorts. He had taken to holing up in his room after work, looking through as many web sites as he could, in the hopes that some tidbit he would uncover would be the trigger for a flash that had some information that would actually produce results. So far, nothing seemed to be popping up – not only was the data in his brain out of date, but as with any unrecalled information in a person's head, certain pieces of information were slowly being forgotten. The entire situation was akin to recalling what someone had for lunch on a particular date a few years ago – details not in constant recall get optimized by the brain.

Chuck's shelf life was beginning to end, and Casey and Walker both knew that his expiration date was rapidly approaching.

* * *

Like many other nerds, Chuck wasn't the most elegant of people. It came as no surprise to Sarah then upon Chuck's less-than-graceful entry into the Weinerlicious. Such was his hurry that he stumbled over the chair closest to the door, and promptly deposited his face onto a floor that she had cleaned only minutes before. Casey's entrance, on the other hand, was like everything else about the NSA agent: calculated, precise, not a single wasted movement. Calmly stepping over the mess that Chuck had created on his way down, he watched with an incredibly satisfied smirk on his face as Chuck peeled himself off of the floor and into a seat after fixing the furniture that he had knocked over. Taking a moment to collect himself, Chuck looked toward the counter where Sarah had watched the entire thing with a raised eyebrow.

"Not a single word, Sarah. I'm already going to be hearing Casey on my case about that for the next day or five, so the avoidance of any additional ridicule would be just great, thanks." Naturally, in addition to the previously raised eyebrow, Sarah's eyes began to twinkle with mischief as well; looking to avert disaster, Chuck quickly continued. "Also, Big Mike wants us back early today, since he's got it in his head that he's not going to meet his sales numbers for the month so he wants the green shirts to move 5 more Supergrill 5000s by next week, and he wants the Herd to sell 15 service plans in that same time, so naturally that translates to Casey and I. So anyway, what's up?"

Ever thankful that the CIA-owned Weinerlicious had no such sales quotas, Sarah motioned the three up to the counter where the video-conferencing equipment was built in, and connected with the NSA office, where Director Graham was manning his usual position right behind General Beckman. The general was the first to speak.

"Agent Walker, Major Casey, Mr. Bartowski, as you've no doubt noticed by now, the data in the Intersect has started to become obsolete. As the second Intersect computer is still in development, we're currently in a position that we can't afford to be in – we have the data, but we need a way to process and link the information. Because of this situation that we find ourselves in, we've come up with a solution which Director Graham will brief you regarding the details."

"We've arranged for Chuck to view another set of encoded images that will provide him with the latest intelligence, which should eliminate any data-related errors in his flashes. A specialist is being flown in this evening to make sure there are no problems with the upload. Agent Walker has further details on how everything will be set up tonight. The upload shouldn't take longer than five minutes, with a few tests afterwards. Agent Walker is to provide us with a status report as soon as the process is complete."

After signing off, Chuck had a slightly concerned look on his face. "How do we know that this won't be like that Zarnow guy? If you remember, that one didn't turn out so well. I almost crashed a helicopter that night."

"But you didn't, Chuck, and that's what matters. While we will be doing this in the Buy More theater room again, we'll be taking extra precautions with 'Patient X' this time to make sure that doesn't happen again. Rest assured, nothing will happen to you. Don't worry at all, you'll be fine."

"If something does happen, maybe you'll learn to stay in the car this time." Such was typical of Casey – snarky comment followed by a grunt and a smirk.

Grumbling about federal agents who had nothing better to do than be disparaging while standing there looking all tough with his thumbs in his belt, Chuck followed Casey out of the Weinerlicious, but not before flashing Sarah one small resigned smile before stepping out of the door.

* * *

A few hours later found Chuck sitting in the home theater room, curtains all drawn, with Casey setting up the display equipment outside just as Sarah walked into the store with a middle-aged woman in tow. She carried a small attaché case with her, from which she produced a small handheld computer that she hooked up. Upon making sure that everything was hooked up and working correctly, she ran the program which flashed thousands of images in rapid succession on the TV set up in the home theater room. After confirming that the upload was complete and the woman was dropped off at the airport, Sarah picked up the phone.

"Walker, secure. The update is complete."

"There didn't seem to be any complications."

"Yes sir, she's in the airport now, and her flight should be heading back to DC within the hour."

"Understood."

As the Porsche pulled away from the curb, Sarah didn't see the woman pull a phone from her jacket to make her own call.

"This is Fae. I wasn't able to get a look at the target, but the Intersect information has been uploaded as planned. The tests proved that everything is working as planned, and we still retain the upper hand. It's probably a good thing that the target did not get to see my face, who knows what information they would've found out. Everything's in place, we'll be moving on to the second phase soon. I'm on my way back now, we'll talk more when I arrive."

* * *

_End Chapter 1._

* * *

_Didn't intend for this chapter to end this way, but halfway through it took a life of its own and this ended up being a good break point._ _Thanks for reading._

_10/29/2008  
_


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